data_7YGP # _entry.id 7YGP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.368 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 7YGP pdb_00007ygp 10.2210/pdb7ygp/pdb WWPDB D_1300030886 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7YGP _pdbx_database_status.recvd_initial_deposition_date 2022-07-12 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kondo, J.' 1 0000-0002-5682-3685 'Torigoe, H.' 2 ? 'Arakawa, F.' 3 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Inorg.Biochem. _citation.journal_id_ASTM JIBIDJ _citation.journal_id_CSD 0525 _citation.journal_id_ISSN 0162-0134 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 241 _citation.language ? _citation.page_first 112125 _citation.page_last 112125 _citation.title 'Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.jinorgbio.2023.112125 _citation.pdbx_database_id_PubMed 36716510 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Torigoe, H.' 1 ? primary 'Kondo, J.' 2 ? primary 'Arakawa, F.' 3 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 7YGP _cell.details ? _cell.formula_units_Z ? _cell.length_a 36.672 _cell.length_a_esd ? _cell.length_b 36.672 _cell.length_b_esd ? _cell.length_c 54.990 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 6 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 7YGP _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*GP*GP*AP*CP*CP*TP*(OHU)P*GP*GP*TP*CP*C)-3') ; 3656.351 1 ? ? ? ? 2 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 1 ? ? ? ? 3 non-polymer syn 'COBALT (II) ION' 58.933 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DG)(DA)(DC)(DC)(DT)(OHU)(DG)(DG)(DT)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GGACCTXGGTCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DG n 1 3 DA n 1 4 DC n 1 5 DC n 1 6 DT n 1 7 OHU n 1 8 DG n 1 9 DG n 1 10 DT n 1 11 DC n 1 12 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 12 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7YGP _struct_ref.pdbx_db_accession 7YGP _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7YGP _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7YGP _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 12 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight CO non-polymer . 'COBALT (II) ION' ? 'Co 2' 58.933 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 OHU 'DNA linking' n ;2'-deoxy-5-hydroxyuridine 5'-(dihydrogen phosphate) ; ? 'C9 H13 N2 O9 P' 324.181 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7YGP _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.92 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 57.87 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'MPD, lithium chloride, hexammine cobalt chloride, Sodium cacodylate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2018-03-15 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00835 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-17A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.00835 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 59.170 _reflns.entry_id 7YGP _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.9970 _reflns.d_resolution_low 20.787 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 5348 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 95.100 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 2.655 _reflns.pdbx_Rmerge_I_obs 0.026 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 17.440 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.987 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.032 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? _reflns.pdbx_CC_split_method ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 2.000 2.050 ? 2.070 ? 1127 449 ? 417 92.900 ? ? ? ? 0.396 ? ? ? ? ? ? ? ? 2.703 ? ? ? ? 0.486 ? ? 1 1 0.842 ? ? ? ? ? ? ? ? ? ? 2.050 2.110 ? 3.100 ? 1029 398 ? 380 95.500 ? ? ? ? 0.279 ? ? ? ? ? ? ? ? 2.708 ? ? ? ? 0.342 ? ? 2 1 0.927 ? ? ? ? ? ? ? ? ? ? 2.110 2.170 ? 3.500 ? 959 371 ? 346 93.300 ? ? ? ? 0.250 ? ? ? ? ? ? ? ? 2.772 ? ? ? ? 0.305 ? ? 3 1 0.964 ? ? ? ? ? ? ? ? ? ? 2.170 2.230 ? 4.500 ? 978 392 ? 369 94.100 ? ? ? ? 0.156 ? ? ? ? ? ? ? ? 2.650 ? ? ? ? 0.190 ? ? 4 1 0.987 ? ? ? ? ? ? ? ? ? ? 2.230 2.310 ? 6.680 ? 932 378 ? 352 93.100 ? ? ? ? 0.113 ? ? ? ? ? ? ? ? 2.648 ? ? ? ? 0.138 ? ? 5 1 0.989 ? ? ? ? ? ? ? ? ? ? 2.310 2.390 ? 8.530 ? 861 346 ? 336 97.100 ? ? ? ? 0.083 ? ? ? ? ? ? ? ? 2.562 ? ? ? ? 0.102 ? ? 6 1 0.995 ? ? ? ? ? ? ? ? ? ? 2.390 2.480 ? 11.040 ? 964 363 ? 350 96.400 ? ? ? ? 0.065 ? ? ? ? ? ? ? ? 2.754 ? ? ? ? 0.078 ? ? 7 1 0.997 ? ? ? ? ? ? ? ? ? ? 2.480 2.580 ? 16.460 ? 799 300 ? 290 96.700 ? ? ? ? 0.048 ? ? ? ? ? ? ? ? 2.755 ? ? ? ? 0.058 ? ? 8 1 0.997 ? ? ? ? ? ? ? ? ? ? 2.580 2.700 ? 17.460 ? 921 342 ? 328 95.900 ? ? ? ? 0.039 ? ? ? ? ? ? ? ? 2.808 ? ? ? ? 0.047 ? ? 9 1 0.999 ? ? ? ? ? ? ? ? ? ? 2.700 2.830 ? 21.500 ? 799 310 ? 299 96.500 ? ? ? ? 0.039 ? ? ? ? ? ? ? ? 2.672 ? ? ? ? 0.047 ? ? 10 1 0.998 ? ? ? ? ? ? ? ? ? ? 2.830 2.980 ? 25.440 ? 686 271 ? 261 96.300 ? ? ? ? 0.035 ? ? ? ? ? ? ? ? 2.628 ? ? ? ? 0.042 ? ? 11 1 0.998 ? ? ? ? ? ? ? ? ? ? 2.980 3.160 ? 29.490 ? 688 283 ? 273 96.500 ? ? ? ? 0.024 ? ? ? ? ? ? ? ? 2.520 ? ? ? ? 0.028 ? ? 12 1 0.999 ? ? ? ? ? ? ? ? ? ? 3.160 3.380 ? 32.450 ? 600 255 ? 244 95.700 ? ? ? ? 0.024 ? ? ? ? ? ? ? ? 2.459 ? ? ? ? 0.029 ? ? 13 1 0.999 ? ? ? ? ? ? ? ? ? ? 3.380 3.650 ? 34.750 ? 606 255 ? 240 94.100 ? ? ? ? 0.023 ? ? ? ? ? ? ? ? 2.525 ? ? ? ? 0.028 ? ? 14 1 0.999 ? ? ? ? ? ? ? ? ? ? 3.650 4.000 ? 35.720 ? 557 216 ? 208 96.300 ? ? ? ? 0.021 ? ? ? ? ? ? ? ? 2.678 ? ? ? ? 0.025 ? ? 15 1 0.999 ? ? ? ? ? ? ? ? ? ? 4.000 4.470 ? 37.360 ? 494 192 ? 182 94.800 ? ? ? ? 0.024 ? ? ? ? ? ? ? ? 2.714 ? ? ? ? 0.030 ? ? 16 1 0.998 ? ? ? ? ? ? ? ? ? ? 4.470 5.160 ? 36.610 ? 435 176 ? 169 96.000 ? ? ? ? 0.021 ? ? ? ? ? ? ? ? 2.574 ? ? ? ? 0.026 ? ? 17 1 0.998 ? ? ? ? ? ? ? ? ? ? 5.160 6.320 ? 36.030 ? 348 150 ? 142 94.700 ? ? ? ? 0.025 ? ? ? ? ? ? ? ? 2.451 ? ? ? ? 0.031 ? ? 18 1 0.998 ? ? ? ? ? ? ? ? ? ? 6.320 8.940 ? 36.040 ? 274 114 ? 108 94.700 ? ? ? ? 0.028 ? ? ? ? ? ? ? ? 2.537 ? ? ? ? 0.037 ? ? 19 1 0.996 ? ? ? ? ? ? ? ? ? ? 8.940 20.787 ? 36.940 ? 140 65 ? 54 83.100 ? ? ? ? 0.025 ? ? ? ? ? ? ? ? 2.593 ? ? ? ? 0.032 ? ? 20 1 0.998 ? ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max 108.240 _refine.B_iso_mean 60.4473 _refine.B_iso_min 47.660 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 7YGP _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.9970 _refine.ls_d_res_low 20.7870 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 5336 _refine.ls_number_reflns_R_free 529 _refine.ls_number_reflns_R_work 4807 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 94.8300 _refine.ls_percent_reflns_R_free 9.9100 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2194 _refine.ls_R_factor_R_free 0.2254 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2186 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.380 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 41.6300 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.3500 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id final _refine_hist.details ? _refine_hist.d_res_high 1.9970 _refine_hist.d_res_low 20.7870 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 250 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total 12 _refine_hist.pdbx_B_iso_mean_ligand 85.42 _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 242 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.008 ? 276 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.153 ? 430 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.045 ? 46 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.005 ? 12 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 19.079 ? 110 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 1.9970 2.1974 . . 136 1184 93.0000 . . . 0.5147 0.0000 0.4347 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.1974 2.5149 . . 129 1186 95.0000 . . . 0.3901 0.0000 0.3602 . . . . . . . . . . . 'X-RAY DIFFRACTION' 2.5149 3.1667 . . 136 1218 96.0000 . . . 0.3272 0.0000 0.2924 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.1667 20.7870 . . 128 1219 95.0000 . . . 0.1691 0.0000 0.1681 . . . . . . . . . . . # _struct.entry_id 7YGP _struct.title 'DNA duplex containing 5OHU-T base pairs' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7YGP _struct_keywords.text 'DNA, metal-mediated base pair, metallo-DNA, mercury' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DT 6 "O3'" ? ? ? 1_555 A OHU 7 P ? ? A DT 6 A OHU 7 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale2 covale one ? A OHU 7 "O3'" ? ? ? 1_555 A DG 8 P ? ? A OHU 7 A DG 8 1_555 ? ? ? ? ? ? ? 1.620 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 12 N3 ? ? A DG 1 A DC 12 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 12 O2 ? ? A DG 1 A DC 12 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 12 N4 ? ? A DG 1 A DC 12 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DC 11 N3 ? ? A DG 2 A DC 11 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DC 11 O2 ? ? A DG 2 A DC 11 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 11 N4 ? ? A DG 2 A DC 11 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 A DT 10 N3 ? ? A DA 3 A DT 10 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DT 10 O4 ? ? A DA 3 A DT 10 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 4 A DG 9 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 4 A DG 9 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 4 A DG 9 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 8 N1 ? ? A DC 5 A DG 8 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 8 O6 ? ? A DC 5 A DG 8 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 8 N2 ? ? A DC 5 A DG 8 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 6 N3 ? ? ? 1_555 A OHU 7 O4 ? ? A DT 6 A OHU 7 6_765 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog16 hydrog ? ? A DT 6 O2 ? ? ? 1_555 A OHU 7 N3 ? ? A DT 6 A OHU 7 6_765 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog17 hydrog ? ? A OHU 7 N3 ? ? ? 1_555 A DT 6 O2 ? ? A OHU 7 A DT 6 6_765 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog18 hydrog ? ? A OHU 7 O4 ? ? ? 1_555 A DT 6 N3 ? ? A OHU 7 A DT 6 6_765 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog19 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 8 A DC 5 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 8 A DC 5 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 8 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 8 A DC 5 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 4 N3 ? ? A DG 9 A DC 4 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 4 O2 ? ? A DG 9 A DC 4 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 4 N4 ? ? A DG 9 A DC 4 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 10 N3 ? ? ? 1_555 A DA 3 N1 ? ? A DT 10 A DA 3 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 10 O4 ? ? ? 1_555 A DA 3 N6 ? ? A DT 10 A DA 3 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 A DG 2 N1 ? ? A DC 11 A DG 2 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 A DG 2 O6 ? ? A DC 11 A DG 2 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 A DG 2 N2 ? ? A DC 11 A DG 2 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 12 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 12 A DG 1 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DC 12 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 12 A DG 1 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DC 12 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 12 A DG 1 6_765 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 7YGP _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.027269 _atom_sites.fract_transf_matrix[1][2] 0.015744 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.031487 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.018185 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C CO N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG DG A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 OHU 7 7 7 OHU 6HU A . n A 1 8 DG 8 8 8 DG DG A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DC 12 12 12 DC DC A . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email j.kondo@sophia.ac.jp _pdbx_contact_author.name_first Jiro _pdbx_contact_author.name_last Kondo _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-5682-3685 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NCO 1 101 51 NCO NCO A . C 3 CO 1 102 1 CO CO A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1880 ? 1 MORE -25 ? 1 'SSA (A^2)' 4400 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 6_765 -x+2,-x+y+1,-z+1/3 -0.5000000000 -0.8660254038 0.0000000000 55.0080000000 -0.8660254038 0.5000000000 0.0000000000 31.7588836076 0.0000000000 0.0000000000 -1.0000000000 18.3300000000 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2023-05-24 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.27 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _pdbx_entry_details.entry_id 7YGP _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7YGP 'double helix' 7YGP 'a-form double helix' 7YGP 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 A DC 12 6_765 -0.179 -0.268 0.373 -1.409 -8.084 0.065 1 A_DG1:DC12_A A 1 ? A 12 ? 19 1 1 A DG 2 1_555 A DC 11 6_765 -0.257 -0.186 -0.218 -12.438 -12.325 2.422 2 A_DG2:DC11_A A 2 ? A 11 ? 19 1 1 A DA 3 1_555 A DT 10 6_765 0.221 -0.243 -0.267 -8.241 -7.672 -3.740 3 A_DA3:DT10_A A 3 ? A 10 ? 20 1 1 A DC 4 1_555 A DG 9 6_765 0.281 -0.129 0.019 5.974 -10.854 3.092 4 A_DC4:DG9_A A 4 ? A 9 ? 19 1 1 A DC 5 1_555 A DG 8 6_765 0.327 -0.253 -0.154 9.413 -3.358 2.301 5 A_DC5:DG8_A A 5 ? A 8 ? 19 1 1 A DT 6 1_555 A OHU 7 6_765 1.552 -2.254 -0.269 -0.055 -23.664 3.303 6 A_DT6:OHU7_A A 6 ? A 7 ? 16 1 1 A OHU 7 1_555 A DT 6 6_765 -1.552 -2.254 -0.269 0.055 -23.664 3.303 7 A_OHU7:DT6_A A 7 ? A 6 ? 16 1 1 A DG 8 1_555 A DC 5 6_765 -0.327 -0.253 -0.154 -9.413 -3.358 2.301 8 A_DG8:DC5_A A 8 ? A 5 ? 19 1 1 A DG 9 1_555 A DC 4 6_765 -0.281 -0.129 0.019 -5.974 -10.854 3.092 9 A_DG9:DC4_A A 9 ? A 4 ? 19 1 1 A DT 10 1_555 A DA 3 6_765 -0.221 -0.243 -0.267 8.241 -7.672 -3.740 10 A_DT10:DA3_A A 10 ? A 3 ? 20 1 1 A DC 11 1_555 A DG 2 6_765 0.257 -0.186 -0.218 12.438 -12.325 2.422 11 A_DC11:DG2_A A 11 ? A 2 ? 19 1 1 A DC 12 1_555 A DG 1 6_765 0.179 -0.268 0.373 1.409 -8.084 0.065 12 A_DC12:DG1_A A 12 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 A DC 12 6_765 A DG 2 1_555 A DC 11 6_765 0.063 -1.148 3.469 5.164 4.975 37.845 -2.383 0.572 3.277 7.587 -7.875 38.494 1 AA_DG1DG2:DC11DC12_AA A 1 ? A 12 ? A 2 ? A 11 ? 1 A DG 2 1_555 A DC 11 6_765 A DA 3 1_555 A DT 10 6_765 -0.304 -0.747 3.210 1.146 4.035 35.310 -1.792 0.659 3.098 6.624 -1.881 35.551 2 AA_DG2DA3:DT10DC11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A DA 3 1_555 A DT 10 6_765 A DC 4 1_555 A DG 9 6_765 0.831 -1.179 2.967 -2.376 12.535 31.151 -3.748 -1.762 2.270 22.210 4.210 33.603 3 AA_DA3DC4:DG9DT10_AA A 3 ? A 10 ? A 4 ? A 9 ? 1 A DC 4 1_555 A DG 9 6_765 A DC 5 1_555 A DG 8 6_765 -0.550 -1.866 3.140 -2.511 7.511 26.096 -5.633 0.609 2.553 16.167 5.404 27.251 4 AA_DC4DC5:DG8DG9_AA A 4 ? A 9 ? A 5 ? A 8 ? 1 A DC 5 1_555 A DG 8 6_765 A DT 6 1_555 A OHU 7 6_765 0.285 -0.855 3.459 6.458 12.855 41.348 -2.419 0.255 3.083 17.578 -8.831 43.676 5 AA_DC5DT6:OHU7DG8_AA A 5 ? A 8 ? A 6 ? A 7 ? 1 A DT 6 1_555 A OHU 7 6_765 A OHU 7 1_555 A DT 6 6_765 0.000 -2.157 3.064 0.000 15.926 17.197 -9.025 0.000 0.802 43.094 0.000 23.398 6 AA_DT6OHU7:DT6OHU7_AA A 6 ? A 7 ? A 7 ? A 6 ? 1 A OHU 7 1_555 A DT 6 6_765 A DG 8 1_555 A DC 5 6_765 -0.285 -0.855 3.459 -6.458 12.855 41.348 -2.419 -0.255 3.083 17.578 8.831 43.676 7 AA_OHU7DG8:DC5DT6_AA A 7 ? A 6 ? A 8 ? A 5 ? 1 A DG 8 1_555 A DC 5 6_765 A DG 9 1_555 A DC 4 6_765 0.550 -1.866 3.140 2.511 7.511 26.096 -5.633 -0.609 2.553 16.167 -5.404 27.251 8 AA_DG8DG9:DC4DC5_AA A 8 ? A 5 ? A 9 ? A 4 ? 1 A DG 9 1_555 A DC 4 6_765 A DT 10 1_555 A DA 3 6_765 -0.831 -1.179 2.967 2.376 12.535 31.151 -3.748 1.762 2.270 22.210 -4.210 33.603 9 AA_DG9DT10:DA3DC4_AA A 9 ? A 4 ? A 10 ? A 3 ? 1 A DT 10 1_555 A DA 3 6_765 A DC 11 1_555 A DG 2 6_765 0.304 -0.747 3.210 -1.146 4.035 35.310 -1.792 -0.659 3.098 6.624 1.881 35.551 10 AA_DT10DC11:DG2DA3_AA A 10 ? A 3 ? A 11 ? A 2 ? 1 A DC 11 1_555 A DG 2 6_765 A DC 12 1_555 A DG 1 6_765 -0.063 -1.148 3.469 -5.164 4.975 37.845 -2.383 -0.572 3.277 7.587 7.875 38.494 11 AA_DC11DC12:DG1DG2_AA A 11 ? A 2 ? A 12 ? A 1 ? # _pdbx_audit_support.funding_organization 'Japan Society for the Promotion of Science (JSPS)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 18K19308 _pdbx_audit_support.ordinal 1 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id OHU _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id OHU _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT HEXAMMINE(III)' NCO 3 'COBALT (II) ION' CO # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #